AMBER Archive (2009)

Subject: Re: [AMBER] From DLG to Antechamber

From: Jack Shultz (js_at_drugdiscoveryathome.com)
Date: Fri Jun 19 2009 - 07:27:20 CDT

Thanks Francois,
Any suggestions on how to add these hydrogens?

Jack

On Fri, Jun 19, 2009 at 5:26 AM, FyD <fyd_at_q4md-forcefieldtools.org> wrote:

> Dear Jack,
>
> After a quick look, it seems you need to add the hydrogens to your
> structure.
>
> regards, Francois
>
>
>
> I'm trying to figure out how to extract a ligand from our docking log
>> file such that it will be compatible with amber. I grepped the
>> receptor-ligand complex for just the ligand file and successfully
>> opened it in PyMole but antechamber is not successful converting to
>> mol2.
>>
>> If I write_all_complexes.py
>> then grep LIG fzd2_ligand_0.pdbqt > fzd2_ligand_0.pdb
>>
>> [boincadm_at_vps receptor]$ cat fzd2_ligand_0.pdb
>> ATOM 1 C LIG d 1 -8.564 -6.344 8.959 0.00 0.00
>> 0.052 A
>> ATOM 2 C LIG d 1 -8.353 -7.525 8.238 0.00 0.00
>> 0.080 A
>> ATOM 3 C LIG d 1 -8.898 -8.731 8.694 0.00 0.00
>> 0.040 A
>> ATOM 4 C LIG d 1 -9.656 -8.756 9.871 0.00 0.00
>> 0.032 A
>> ATOM 5 C LIG d 1 -9.868 -7.575 10.591 0.00 0.00
>> 0.036 A
>> ATOM 6 C LIG d 1 -9.322 -6.369 10.136 0.00 0.00
>> 0.048 A
>> ATOM 7 N LIG d 1 -10.633 -7.600 11.782 0.00 0.00
>> -0.323 N
>> ATOM 8 C LIG d 1 -10.097 -8.061 12.908 0.00 0.00
>> 0.257 C
>> ATOM 9 O LIG d 1 -8.941 -8.479 12.913 0.00 0.00
>> -0.267 OA
>> ATOM 10 H LIG d 1 -11.588 -7.268 11.775 0.00 0.00
>> 0.169 HD
>> ATOM 11 C LIG d 1 -10.892 -8.069 14.157 0.00 0.00
>> 0.043 A
>> ATOM 12 C LIG d 1 -11.303 -6.861 14.733 0.00 0.00
>> -0.010 A
>> ATOM 13 C LIG d 1 -12.054 -6.868 15.914 0.00 0.00
>> -0.025 A
>> ATOM 14 C LIG d 1 -10.962 -5.645 14.127 0.00 0.00
>> 0.013 A
>> ATOM 15 C LIG d 1 -12.395 -8.083 16.519 0.00 0.00
>> 0.012 A
>> ATOM 16 C LIG d 1 -12.464 -5.660 16.490 0.00 0.00
>> 0.012 A
>> ATOM 17 C LIG d 1 -11.984 -9.291 15.944 0.00 0.00
>> 0.002 A
>> ATOM 18 C LIG d 1 -11.232 -9.284 14.762 0.00 0.00
>> 0.018 A
>> ATOM 19 C LIG d 1 -12.124 -4.444 15.884 0.00 0.00
>> 0.001 A
>> ATOM 20 C LIG d 1 -11.373 -4.437 14.703 0.00 0.00
>> 0.001 A
>> ATOM 21 C LIG d 1 -7.987 -5.069 8.478 0.00 0.00
>> 0.183 A
>> ATOM 22 N LIG d 1 -7.556 -4.088 9.248 0.00 0.00
>> -0.221 NA
>> ATOM 23 C LIG d 1 -7.080 -3.046 8.442 0.00 0.00
>> 0.093 A
>> ATOM 24 C LIG d 1 -7.244 -3.448 7.112 0.00 0.00
>> 0.106 A
>> ATOM 25 C LIG d 1 -6.522 -1.794 8.732 0.00 0.00
>> 0.034 A
>> ATOM 26 O LIG d 1 -7.814 -4.719 7.140 0.00 0.00
>> -0.289 OA
>> ATOM 27 C LIG d 1 -6.851 -2.600 6.070 0.00 0.00
>> 0.040 A
>> ATOM 28 C LIG d 1 -6.293 -1.348 6.360 0.00 0.00
>> 0.003 A
>> ATOM 29 C LIG d 1 -6.130 -0.946 7.691 0.00 0.00
>> 0.002 A
>> ATOM 30 O LIG d 1 -7.610 -7.501 7.086 0.00 0.00
>> -0.360 OA
>> ATOM 31 H LIG d 1 -7.659 -6.631 6.659 0.00 0.00
>> 0.217 HD
>> [boincadm_at_vps receptor]$ antechamber -fi pdb -i fzd2_ligand_0.pdb -fo
>> mol2 -o fzd2_ligand_0.mol2
>>
>> Warning: the assigned bond types may be wrong, please :
>> (1) double check the structure (the connectivity) and/or
>> (2) adjust atom valence penalty parameters in APS.DAT, and/or
>> (3) increase MAXVASTATE in define.h and recompile bondtype.C
>> (4) increase PSCUTOFF in define.h and recompile bondtype.C
>> Be cautious, use a large value of PSCUTOFF (>10) will
>> significantly increase the computer time
>> Error: cannot run "/usr/local/antechamber-1.27/exe/bondtype -i
>> ANTECHAMBER_BOND_TYPE.AC0 -o ANTECHAMBER_BOND_TYPE.AC -f ac -j full"
>> in judgebondtype() of antechamber.c properly, exit
>> [boincadm_at_vps receptor]$
>>
>
>
>
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-- 
Jack

http://drugdiscoveryathome.com
http://hydrogenathome.org
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